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NM_000642.3(AGL):c.2309-1G>A

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Jan 7, 2021)
Last evaluated:
Aug 4, 2020
Accession:
VCV000188804.2
Variation ID:
188804
Description:
single nucleotide variant
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NM_000642.3(AGL):c.2309-1G>A

Allele ID
186643
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p21.2
Genomic location
1: 99884119 (GRCh38) GRCh38 UCSC
1: 100349675 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.100349675G>A
NC_000001.11:g.99884119G>A
NG_012865.1:g.39036G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:99884118:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00001
Links
ClinGen: CA273983
dbSNP: rs786204481
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Aug 4, 2020 RCV000169136.2
Pathogenic 1 criteria provided, single submitter Aug 13, 2017 RCV000587290.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
AGL - - GRCh38
GRCh37
1284 1299

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Aug 13, 2017)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease IIIa
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000697530.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (2)
Comment:
Variant summary: The c.2309-1G>A (aka IVS17-1G>A) in a AGL gene is a splice-site variant that alters a highly conserved nucleotide. 5/5 in silico tools via … (more)
Likely pathogenic
(May 27, 2014)
criteria provided, single submitter
Method: literature only
Glycogen storage disease type III
(Autosomal recessive inheritance)
Allele origin: unknown
Counsyl
Accession: SCV000220351.1
Submitted: (Mar 11, 2015)
Evidence details
Publications
PubMed (1)
Likely pathogenic
(Aug 04, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
Invitae
Accession: SCV001575138.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change affects an acceptor splice site in intron 17 of the AGL gene. It is expected to disrupt RNA splicing and likely results … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Cross-sectional retrospective study of muscle function in patients with glycogen storage disease type III. Decostre V Neuromuscular disorders : NMD 2016 PMID: 27460348
Molecular analysis of the AGL gene: identification of 25 novel mutations and evidence of genetic heterogeneity in patients with Glycogen Storage Disease Type III. Goldstein JL Genetics in medicine : official journal of the American College of Medical Genetics 2010 PMID: 20648714
Distinct mutations in the glycogen debranching enzyme found in glycogen storage disease type III lead to impairment in diverse cellular functions. Cheng A Human molecular genetics 2009 PMID: 19299494
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547

Text-mined citations for rs786204481...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021